polymapR (version 1.0.17)

r6_functions: Calculate recombination frequency, LOD and log-likelihood from frequency tables in a random pairing hexaploid

Description

This group of functions is called by linkage.

Usage

r6_1.0_1.0(x)
r6_1.0_1.1(x)
r6_1.0_1.2(x)
r6_1.0_1.3(x)
r6_1.0_1.4(x)
r6_1.0_1.5(x)
r6_1.0_2.0(x)
r6_1.0_2.1(x)
r6_1.0_2.2(x)
r6_1.0_2.3(x)
r6_1.0_2.4(x)
r6_1.0_3.0(x)
r6_1.0_3.1(x)
r6_1.0_3.2(x)
r6_1.0_3.3(x)
r6_1.0_4.1(x)
r6_1.1_1.1(x)
r6_1.1_1.2(x)
r6_1.1_1.3(x)
r6_1.1_1.4(x)
r6_1.1_1.5(x)
r6_1.1_2.0(x)
r6_1.1_2.2(x)
r6_1.1_2.3(x)
r6_1.1_2.4(x)
r6_1.1_3.0(x)
r6_1.1_3.3(x)
r6_1.2_1.2(x)
r6_1.2_1.3(x)
r6_1.2_1.4(x)
r6_1.2_1.5(x)
r6_1.2_2.1(x)
r6_1.2_2.2(x)
r6_1.2_2.3(x)
r6_1.2_2.4(x)
r6_1.2_3.0(x)
r6_1.2_3.1(x)
r6_1.2_3.2(x)
r6_1.2_3.3(x)
r6_1.2_4.1(x)
r6_1.3_1.3(x)
r6_1.3_1.4(x)
r6_1.3_1.5(x)
r6_1.3_2.2(x)
r6_1.3_2.3(x)
r6_1.3_2.4(x)
r6_1.3_3.1(x)
r6_1.3_3.2(x)
r6_1.3_3.3(x)
r6_1.3_4.1(x)
r6_1.4_1.4(x)
r6_1.4_1.5(x)
r6_1.4_2.2(x)
r6_1.4_2.3(x)
r6_1.4_2.4(x)
r6_1.4_3.2(x)
r6_1.4_3.3(x)
r6_1.4_4.1(x)
r6_1.5_1.5(x)
r6_1.5_2.2(x)
r6_1.5_2.3(x)
r6_1.5_2.4(x)
r6_1.5_3.2(x)
r6_1.5_3.3(x)
r6_2.0_1.2(x)
r6_2.0_1.3(x)
r6_2.0_1.4(x)
r6_2.0_1.5(x)
r6_2.0_2.0(x)
r6_2.0_2.1(x)
r6_2.0_2.2(x)
r6_2.0_2.3(x)
r6_2.0_2.4(x)
r6_2.0_3.0(x)
r6_2.0_3.1(x)
r6_2.0_3.2(x)
r6_2.0_3.3(x)
r6_2.0_4.1(x)
r6_2.1_1.5(x)
r6_2.1_2.4(x)
r6_2.1_3.0(x)
r6_2.2_2.2(x)
r6_2.2_2.3(x)
r6_2.2_2.4(x)
r6_2.2_3.2(x)
r6_2.2_3.3(x)
r6_2.3_2.3(x)
r6_2.3_2.4(x)
r6_2.3_3.2(x)
r6_2.3_3.3(x)
r6_2.4_2.4(x)
r6_3.0_1.3(x)
r6_3.0_1.4(x)
r6_3.0_1.5(x)
r6_3.0_2.2(x)
r6_3.0_2.3(x)
r6_3.0_2.4(x)
r6_3.0_3.0(x)
r6_3.0_3.1(x)
r6_3.0_3.2(x)
r6_3.0_3.3(x)
r6_3.0_4.1(x)
r6_3.3_2.4(x)
r6_3.3_3.3(x)
p6_1.0_1.0(x)

Arguments

x

A frequency table of the different classes of dosages in the progeny. The column names start with "n_". Followed by the dosage of the first marker and then of the second.

Value

A list with the following items:

r_mat

A matrix with recombination frequencies for the different phases

LOD_mat

A matrix with LOD scores for the different phases

logL_mat

A matrix with log likelihood ratios for the different phases

phasing_strategy

A character string specifying the phasing strategy. "MLL" for maximum likelihood en "MINR" for minimum recombination frequency.

possible_phases

The phases between markers that are possible. Same order and length as column names of output matrices.